Digital Commons Network^™

A History Of University Of Rhode Island Partnerships In The Philippines With Marine Resources And Fisheries Management As Primary Drivers, Michael A. Rice, Donald D. Robadue, Brian Crawford

Fisheries, Animal and Veterinary Sciences Faculty Publications

No abstract provided.

Centering California’S Black Multilingual Learners: Intersections, Equity, And (In)Visibilities, Ayanna Cooper, Ed.D., Magaly Lavadenz, Ph.D., Elvira G. Armas, Ed.D., Malane Morales Van-Hecke

Education and Policy Briefs

Grounded in an asset-based approach to educational transformation, this education and policy brief presents an exploratory inquiry into Black Multilingual Learners (BMLs) in California, recognizing the intersection of their racial, linguistic, and cultural identities. The inquiry draws on statewide demographic and English language proficiency data, relevant research, student and educator bright spots, and the Young, Bilingual and Black in California Survey of local educational agency representatives. Three key findings emerged: Visibility Gaps in state reporting systems, an Intersectional Data Gap caused by the absence of disaggregated racial data on public-facing data platforms, and an Infrastructure Gap in local data collection …

Spartan Daily, September 1, 2026, San Jose State University, School Of Journalism And Mass Communications

Spartan Daily, 2026

Volume 167, Issue 05

Association Between Estimated Time With Low Glomerular Filtration Rate And Access To Transplant Among Youth With Advanced Chronic Kidney Disease., Elaine Ku, Timothy Copeland, Charles E. Mcculloch, Jonathan D. Savant, Bradley A. Warady, Susan L. Furth, Sarah Kizilbash, Daniel I. Feig, Roshan P. George, Joseph T. Flynn, Judith Jerry-Fluker, Matthew B. Matheson, Sandra Amaral, Ckid Investigators

Manuscripts, Articles, Book Chapters and Other Papers

BACKGROUND: Slower chronic kidney disease (CKD) progression allows more time for transplant preparation. Whether differences in CKD progression by race/ethnicity associate with preemptive or living donor transplantation in youth has not been well studied.

METHODS: We examined the association between time spent with low eGFR (between 10-30 mL/min/1.73 m²) and odds of preemptive or living donor transplantation among youth with CKD. eGFR was estimated using the bedside Schwartz (if < 18 years) and CKD-EPI 2021 equations (if ≥ 18 years) and the CKiD U25 equation in sensitivity analysis. Time spent with low eGFR was compared by race/ethnicity.

RESULTS: Among 333 youth with CKD (median age 11 years [IQR 7,14]), median time spent with low eGFR was 28.8 months. 77% were preemptively waitlisted, and 45% received preemptive …

Prediction Model For Children With Anaphylaxis Who May Not Require Emergency Department Care: A Multicenter Retrospective Cohort Study., Timothy E. Dribin, David Schnadower, Hugh A. Sampson, Yin Zhang, Nanhua Zhang, Stephen B. Freedman, Mark I. Neuman, David C. Brousseau, Rakesh D. Mistry, Stephanie Boyd, Yonatan Wolnerman, Patrick S. Walsh, Craig Vander Wyst, Vandana Thapar, Jonathan Strutt, Geetanjali Srivastava, Nidhi V. Singh, Christopher J. Russo, Christian D. Pulcini, Thuy L. Ngo, Jo-Ann O. Nesiama, Matthew M. Moake, Ashley M. Metcalf, Tamar R. Lubell, Juhee Lee, Chari D. Larsen, Karen Y. Kwan, Curtis L. Knoles, Kajal Khanna, Julia F. Freeman, Justin R. Davis, Alicia Daggett, Joanna S. Cohen, Ari R. Cohen, Wee-Jhong Chua, Sri S. Chinta, Brittany Boswell, Kelly R. Bergmann, Paul L. Aronson, Kenneth A. Michelson

Manuscripts, Articles, Book Chapters and Other Papers

BACKGROUND: The 2023 US Anaphylaxis Practice Parameter indicated that some patients receiving epinephrine in the community might avoid emergency department (ED) visits; however, the criteria and safety of this approach remain unproven.

OBJECTIVE: To derive and validate a clinical prediction model for identifying children at risk of receiving epinephrine after arriving at the ED.

METHODS: We conducted a 31-center retrospective cohort study of children aged 6 months to less than 18 years who received 1 prehospital dose of epinephrine for allergic reactions between 2016 and 2019. The outcome was receipt of epinephrine after ED arrival. We used least absolute shrinkage …

Maternal Violent Injury And Child Exposure To Violence-A Call For Trauma-Informed And Structural Responses., Gunjan Tiyyagura, M Katherine Henry, Kimberly Randell

Manuscripts, Articles, Book Chapters and Other Papers

No abstract provided.

Characteristics Of Individuals With Cerebral Palsy Across The Us., Bhooma R. Aravamuthan, Amy F. Bailes, Micah Baird, Kristie Bjornson, Ira Bowen, Angeline Bowman, Elizabeth R. Boyer, Rose N. Gelineau-Morel, Laurie Glader, Paul H. Gross, Stacey Hall, Edward A. Hurvitz, Michael Kruer, Thomas Larrew, Neena I. Marupudi, Patrick G. Mcphee, Stephen A. Nichols, Garey Noritz, Joyce Oleszek, Justin Ramsey, Jeffrey S. Raskin, Heather Riordan, Brandon G. Rocque, Manish N. Shah, Benjamin J. Shore, M Wade Shrader, David Spence, Charles B. Stevenson, Richard Stevenson, Sruthi P. Thomas, Joyce P. Trost, Stephen R. Wisniewski, Cerebral Palsy Research Network

Manuscripts, Articles, Book Chapters and Other Papers

This cross-sectional study examines how demographics and characteristics of individuals with cerebral palsy across the US associate with Gross Motor Function Classification System level and genetic etiology.

More Than A Free Snack: Benefits Of Mobilized Resources And Socialization For Pediatric Healthcare Workers., Thomas Ayres, Kristin Ray, Aimee M. Hoflander, Angela Myers

Manuscripts, Articles, Book Chapters and Other Papers

INTRODUCTION: Addressing the burnout epidemic in the healthcare workforce is a primary concern of the modern healthcare organization and recognized across researchers and leaders of nations. This study aims to test whether a mobilized micro-break intervention, the Wellbeing on Wheels (WOW) Cart, improved health care worker (HCW) energy perceived organizational support and work engagement.

METHODOLOGY: This study was conducted at an independent children's hospital in the midwestern United States. Between August and September 2024. A total of 367 pediatric HCWs completed our survey. IBM's SPSS was used to analyze the data using t-tests, ANOVAs, linear regression, and polynomial regression …

Diagnostic Delay In Acute Care Settings And The Economic Burden Of Pemphigus And Pemphigoid: A Literature Review, Sana Altaf, Sara Shah, Simran Gill, Sarah Mazurovsky, Yasmeen Magharehabed, Carolyn Duong, Karen Vo

Student Publications

Pemphigus vulgaris (PV), bullous pemphigoid, and paraneoplastic pemphigus are autoimmune blistering diseases carrying significant mortality risk and economic burden. Diagnosis is frequently delayed in acute care settings, where these conditions mimic common dermatoses such as cellulitis, aphthous stomatitis, and Stevens-Johnson syndrome/toxic epidermal necrolysis. While emergency departments appropriately triage and admit severely affected patients, definitive diagnosis is often delayed across the acute care continuum, averaging 6 to 12 months from symptom onset. These delays result in repeated visits, inappropriate therapies, and avoidable hospitalizations. Pemphigus vulgaris hospitalization costs average $14,500 per patient annually in the United States, and cellulitis misdiagnosis alone generates …

Predictive Modeling For Traffic Accident Severity Using Machine Learning, Ahmad Bin Eid

Theses

Road traffic accidents remain a persistent public safety challenge, responsible for over 1.3 million deaths annually according to the World Health Organization. While considerable effort has gone into understanding accident patterns, predicting the severity of an accident before or immediately after it occurs remains a difficult problem — particularly when the underlying data is messy, imbalanced, and largely categorical in nature. This study applies three supervised machine learning classification algorithms — Logistic Regression, Random Forest, and Gradient Boosting — to predict the severity of road traffic accidents using a dataset of 12,316 records collected by the Addis Ababa Sub-city Police …

Workload-Aware Performance Prediction And Data Movement For Data-Intensive Computing, Kevin Assogba

Theses

Data-intensive workloads in high-performance computing and artificial intelligence move massive volumes of data across deep memory and storage hierarchies, often spending more time moving data than computing on it. Their access patterns, data-sharing relationships, and computational graph properties are largely determined by descriptors known to the application before execution. However, general-purpose runtimes treat this structure as opaque, and the resulting gap between workload behavior and runtime decisions accounts for a substantial fraction of their execution time. Despite advances in performance modeling and data-movement systems, this structure remains underexploited. Schedulers, caches, and I/O paths provision resources conservatively, prediction models are rarely …

Greennet: Ai-Driven Routing Simulator For Sustainable Internet Energy Optimization, Olta Zagraxha

Theses

Reducing the energy consumption of communication networks while maintaining reliable service is an important challenge in sustainable computing. This capstone presents GreenNet, a simulation and evaluation framework designed to investigate whether energy-aware network control can reduce estimated energy consumption without unacceptable degradation in Quality of Service (QoS). GreenNet combines a graph-based network simulator, configurable traffic scenarios, and a web-based interface for examining network behavior and comparing control strategies. Three approaches are evaluated: an All-On baseline that keeps all links active, a rule-based heuristic that selectively deactivates links, and a hybrid controller based on Proximal Policy Optimization (PPO), whose proposed actions …

Characteristics Of Individuals With Cerebral Palsy Across The Us, Bhooma R Aravamuthan, Et Al.

2020-Current year OA Pubs

No abstract provided.

Abundance And Balance Of Circulating Leukocyte Subsets And Colorectal Cancer Survival, Alicia R Richards, Maria F Gomez, Bianca I Dowling, Catherine M Bulka, Biljana Gigic, Jane C Figueiredo, Christopher I Li, David Shibata, Adetunji T Toriola, Doratha A Byrd, Cornelia M Ulrich, Mingxiang Teng, Paul A Stewart, Erin M Siegel, Jacob K Kresovich

2020-Current year OA Pubs

BACKGROUND: Cancer immunology research has traditionally focused on tumor-infiltrating leukocytes, but the role of the peripheral leukocytes remains understudied. Since tumor-infiltrating leukocytes are recruited from the blood, circulating immune profiles may provide prognostic insights obtainable before surgery, reflecting overall immune competence.

METHODS: We analyzed treatment-naïve blood samples from 134 stage I-III colorectal cancer (CRC) patients using a nested case-control design (33 recurrences, 45 deaths; median follow-up: 7.4 years). Circulating leukocyte subsets were estimated using methylation cytometry applied to genome-wide methylation profiles. Cox regression models estimated associations between leukocyte metrics and disease-free and overall survival, adjusting for clinical factors.

RESULTS: Higher …

Genomic Analysis Of Oesophageal Carcinoma (Ec) Identifies Recurrent Mutations In Histone Methyltransferases As A Distinctive Subset, Jingyuan Wang, Moh'd Khushman, Et Al.

2020-Current year OA Pubs

Histone-lysine N-methyltransferase 2 (KMT2) family proteins methylate lysine 4 on the histone H3 tail at important regulatory regions in the genome and thereby impart crucial functions through modulating chromatin structures and DNA accessibility. We aimed to identify the molecular profile of KMT2-MT oesophageal cancer (EC) and associations with patient outcomes. In our study, KMT2 mutations were significantly associated with longer immunotherapy-related overall survival (OS) in the esophageal adenocarcinoma (EA) (21.42 vs 13.42 months, HR = 0.66, 95% CI: 0.50-0.88, P = 0.004), but not in the esophageal squamous cell carcinoma (ESCC). KMT2 mutations were significantly associated with microsatellite instability-high and …

Satisfaction And Treatment Burden Among Early Adopters Of Long-Acting Injectable Cabotegravir-Rilpivirine With And Without Viremia In Three Us Ryan White Clinics, Katerina A Christopoulos, Caleb Mccracken, Aaloke Mody, Et Al.

2020-Current year OA Pubs

Among underserved people with HIV with a median of one year of long-acting cabotegravir-rilpivirine use, including those starting with viremia due to adherence challenges, we found higher satisfaction and lower treatment burden compared to daily oral ART, although nearly half preferred another dosing modality and/or a longer dosing interval.

The Impact Of Global Imbalance On Pelvic Fixation Failure: A Single Institution Matched Case-Control Study, Karan Joseph, Samuel Vogl, Jeffrey T Galla, Alexander T Yahanda, Vivek P Gupta, Salim Yakdan, Miguel A Ruiz-Cardozo, Benjamin Plog, Tim Bui, Noah D Poulin, Sundeep Chakladar, Francisco Narro-Garcia, Jason Ng, Matthew Wang, Braeden Benedict, Samuel Brehm, Hana Hallak, Karma Barot, Nicholas Pallotta, Munish C Gupta, Brian J Neuman, Jacob K Greenberg, Wilson Z Ray, Camilo A Molina

2020-Current year OA Pubs

Study DesignRetrospective matched case-control study.ObjectivesPelvic fixation failure (PFF) is a rare, underrecognized mechanical complication from surgical management of adult spinal deformity (ASD). Studies show that residual postoperative malalignment may increase mechanical stress on pelvic instrumentation, but the role of global radiographic parameters in predicting PFF remains poorly defined. Our study aims to identify radiographic predictors of PFF and evaluate the time-dependent relationship between residual deformity and PFF rates.MethodsThis was a single-center, retrospective, matched case-control study of ASD patients who underwent pelvic fixation from 2016-2024 and had >1-year postoperative follow-up. PFF was defined as any reoperation for pelvic screw or rod …

Sacral U-Type Fractures: A Comparative Study Of Treatment Approaches, Arnaldo Martinez Rivera, Garrison P Bentz, Dillon H Stone, Daniel E Pereira, Jeffrey T Galla, Blake K Montgomery, John C Clohisy, Jenna-Leigh Wilson, Brian J Neuman, Jacob Buchowski, Keith Bridwell, Mitchel R Obey, Anna N Miller, Mark J Lambrechts, Et Al.

2020-Current year OA Pubs

Study DesignRetrospective Cohort Study.ObjectivesTo evaluate clinical and patient reported outcomes between operative and non-operative management strategies for sacral U-type fractures.MethodsThis retrospective review included patients with sacral U-type fractures from a 12-year period at a Level 1 trauma center. Demographic, Modified 5-Item Frailty Index (mFI-5), complications, outcomes, and Patient-Reported Outcomes Measurement Information System (PROMIS) data were collected. Fractures were classified by the AO Spine Sacral Injury Classification System (AOSSIC) and analyzed by subtype and treatment modality (trans-sacral screw fixation (TSF) or lumbopelvic fixation (LPF) vs non-operative). Statistical significance was

Cracking The Code: Genotype-Phenotype Correlation Models In Sarcoglycanopathies, Leonela Luce, Conrad C Weihl, Et Al.

2020-Current year OA Pubs

OBJECTIVE: Sarcoglycanopathies are among the most severe limb-girdle muscular dystrophies (LGMD), though milder presentations have been described. These diseases are primarily caused by missense variants, but the limited predictability of their effect on protein maturation, complex formation, and transport has hindered reliable genotype-phenotype correlations. This study aimed to establish accurate genotype-phenotype correlations for LGMDR3, LGMDR4, and LGMDR5.

METHODS: We analyzed the largest sarcoglycanopathy cohort to date (n = 541). Clinical data, including age at symptom onset and loss of ambulation, were collected and used to define phenotype severity. Predictive models were developed considering the impact of non-truncating variants on secondary …

Opioid Dispensing Volume And Per-Patient Intensity In Sickle Cell Disease, Kevin Y Xu, Brandon K Attell, Joanna L Buss, Tashalee R Brown, Charles R Jonassaint, Richard A Grucza, Allison A King, Max Jordan Nguemeni Tiako

2020-Current year OA Pubs

IMPORTANCE: Opioids remain central to management of acute and chronic pain in sickle cell disease (SCD). Opioid dispensing declined over the 2010s amid opioid stewardship efforts, but patterns since 2020 are less clear. Analyses aggregating opioids into morphine milligram equivalents (MME) may obscure agent-specific patterns.

OBJECTIVE: To characterize opioid dispensing volume and per-recipient frequency, duration, and dose among individuals with SCD.

DESIGN, SETTING, AND PARTICIPANTS: A retrospective cohort study of commercially insured and Medicaid-enrolled patients with SCD using the Merative MarketScan databases across 3 periods from January 2011 to February 2016, March 2016 to December 2020, and January 2021 to …

Parent-Child Neural Dynamics During A Stressful Task: Probing Associations With Temperament And Anxiety, Joscelin Rocha-Hidalgo, Harmony Nguyen, Dakota Reis, Denny Schaedig, Kahlil I Thompson, Susan B Perlman, Koraly E Pérez-Edgar

2020-Current year OA Pubs

Dynamic social interactions between parents and children can contribute to anxiety risk, amplifying shared genetic risk. Research has focused on observed behaviors to explain intergenerational transmission. Neural synchrony may contribute as a biological conduit for behavioral transmission of risk. We examined 109 parent-child dyads (

Spinal Cord Imaging For Multiple Sclerosis: Advances, Priorities, And Opportunities, Cornelia Laule, Matthew R Brier, Et Al.

2020-Current year OA Pubs

The spinal cord plays a central role in the pathophysiology and clinical manifestations of multiple sclerosis (MS), yet remains under-studied compared with the brain. This review summarizes key insights from the 2025 North American Imaging in MS Spinal Cord Imaging Workshop, highlighting recent advances, ongoing challenges, and future opportunities in MS spinal cord imaging. We review pathological studies and outline the clinical relevance of spinal cord lesions and atrophy for diagnosis, prognosis, and disease monitoring, highlighting emerging biomarkers of progression independent of relapse activity. Correlations between magnetic resonance imaging, histopathology, and clinical outcomes support the validation and translational potential of …

Energy Conservation In Mri: Sequence Selection And Operational Strategies, Nathan Scherer, Felicia Wang, Andrew L Chang, Mariam Malik, Anna Schroeder, Heather Craig, Benjamin E Northrup

2020-Current year OA Pubs

RATIONALE AND OBJECTIVES: The healthcare system accounts for approximately 9.8% of the United States' (U.S.) greenhouse gas emissions, much of which is due to imaging, particularly magnetic resonance imaging (MRI). This study investigates the components of MRI energy consumption and compares sequences that may be interchangeable in clinical practice. Although the greatest potential for decreasing energy expenditure lies in reduction of inappropriate imaging and optimizing energy consumption of idle MRI equipment, sequence substitution offers an underexplored solution that can potentially be implemented without changing practice patterns or capital expenditure.

MATERIALS AND METHODS: MRI energy expenditure of one machine was monitored …

Implementation Of A New Mri Contrast Policy At A Large Hospital System: Access To Contrast-Enhanced Mri And Development Of Nsf In Patients With Renal Insufficiency, Daniel R Ludwig, Fan Zhang, Brittany Minor, Tammie L S Benzinger, Anup S Shetty

2020-Current year OA Pubs

RATIONALE AND OBJECTIVES: To evaluate access to contrast-enhanced MRI among patients with acute or chronic renal failure after implementation of a more permissive contrast policy and determine whether any patients developed nephrogenic systemic fibrosis (NSF).

MATERIALS AND METHODS: This retrospective study included all patients who had an order for contrast-enhanced MRI in our healthcare system between July 1st, 2023 and June 30th, 2025. Each exam was categorized as completed or cancelled, and multivariable analysis was performed to identify factors associated with exam cancellation. Potential diagnoses of NSF were identified by searching the problem list and encounter diagnoses using ICD-10 codes. …

Perioperative Depression And Anxiety Care In Older Patients: A Randomized Clinical Trial, Joanna Abraham, Katherine J Holzer, Simon Haroutounian, Bethany Pennington, Ana Baumann, Ryan Calfee, Theresa Cordner, Kenneth E Freedland, Thomas Kannampallil, Benjamin Kozower, Emily Lenard, J Philip Miller, Mary Politi, Michael Yingling, Michael S Avidan, Eric J Lenze

2020-Current year OA Pubs

IMPORTANCE: Depression and anxiety are common among older adults undergoing surgery and are associated with adverse postoperative outcomes. However, effective tailored perioperative mental health interventions are lacking.

OBJECTIVE: To evaluate a perioperative intervention to optimize mental health.

DESIGN, SETTING, AND PARTICIPANTS: A single-blind, hybrid, type 1, effectiveness-implementation randomized clinical trial was conducted (November 1, 2022, to March 31, 2025), with 3-month postoperative follow-up, at a US academic and community practice hospital network. Participants were 60 years or older; scheduled for cardiac, oncologic, or orthopedic surgery; and had clinically meaningful symptoms of depression and/or anxiety based on the Patient Health Questionnaire-Anxiety …

Comparison Of Safety And Efficacy Of Lower-Intensity Versus Standard Unfractionated Heparin Infusion Nomograms For Extracranial Venous Thromboembolism In The Neurological Intensive Care Unit, Abdullah M Hakoun, Megha Gupta, Rajat Dhar, Mahta Mardani, Fatih Koc, Salah G Keyrouz

2020-Current year OA Pubs

BACKGROUND: Anticoagulation for acute venous thromboembolism (VTE) in the neurological intensive care unit is challenging because patients with acute brain injury or recent neurosurgery are at high risk for hemorrhagic complications. Unfractionated heparin infusions are commonly used, sometimes with lower activated partial thromboplastin time targets, but the safety and effectiveness of lower-intensity UFH nomograms remain poorly defined.

METHODS: We performed a retrospective single-center study of patients diagnosed with acute extracranial VTE, including deep venous thrombosis and/or pulmonary embolism, between June 2018 and April 2024. Patients were grouped by treatment strategy: standard-intensity UFH targeting aPTT 60-100 s, lower-intensity UFH targeting aPTT …

Pediatric Hypertension Prevalence With 1 Vs. 2 Vs. 3 Within-Visit Blood Pressure Readings (Nhanes 2013-2020), Sandeep K Riar, Donald L Batisky, Scott Gillespie, Andrew M South

2020-Current year OA Pubs

To compare hypertension prevalence using 'initial' blood pressure (BP), 'subsequent' BP (averaged second and third readings) and 'total' BP (averaged three readings), we included 8-17-year-old youth with three BP readings from NHANES 2013-2020. From 2013-2016, BP was obtained using auscultation (manual protocol, MP) and subsequently, using oscillometry (automated protocol, AP). We excluded subjects with 'zero' diastolic blood pressure (DBP). In 5656 subjects, clinical hypertension (high systolic blood pressure [SBP] and/or DBP) prevalence was highest with 'initial' BP (350/5 642, 6.2% [95% CI 5.6-6.9%]), lower with 'subsequent' BP (289/5 642, 5.1% [4.6-5.7%], p <  0.001), and lowest with 'total' BP (251/5 642, 4.4% [3.9-5.0%], p <  0.001). Both MP and AP groups maintained this trend with a significantly lower hypertension prevalence with 'total' vs. 'subsequent' BP. An exception to the trend occurred in the AP group for three conditions: diastolic hypertension, hypertension in high BMI and Hispanic subjects. Diastolic hypertension prevalence with 'subsequent' DBP (86/2 285, 3.8% [3.1-4.6%]) exceeded that with 'initial' DBP (83/2 285, 3.6% [2.9-4.5%]) and was lowest with 'total' DBP (59/2 285, 2.6% [2.0-3.3%]). Diastolic hypertension prevalence was higher (126/5 642, 2.2% [1.9 - 2.7%]) with the 2016 European guidelines (same as 'subsequent' DBP) than with 'total' DBP (94/5 642, 1.7% [1.4 - 2.0%]). Our findings support the inclusion of the first BP reading in BP categorization, as 'total BP' leads to lower hypertension classification than 'subsequent' BP.

Pda (Privacy-Preserving Distributed Algorithms) In Action: Ten Principles For High-Quality Multi-Site Clinical Evidence Generation, Yong Chen, Chongliang Luo, Et Al.

2020-Current year OA Pubs

BACKGROUND: Distributed Research Networks (DRNs) offer significant opportunities for collaborative multi-site research and have significantly advanced healthcare research based on clinical observational data. However, generating high-quality real-world evidence using fit-for-use data from multi-site studies faces important challenges, including biases associated with various types of heterogeneity within and across sites and data sharing difficulties. Over the last 10 years, Privacy-Preserving Distributed Algorithms (PDA) have been developed and utilized in numerous national and international real-world studies spanning diverse domains, from comparative effectiveness research, target trial emulation, to healthcare delivery, policy evaluation, and system performance assessment. Despite these advances, there remains a lack …

Irs: Iterative Reference Selection Improves Normalization Of Microbiome Sequencing Data, Yiming Shi, Lili Liu, Jun Chen, Kristine M Wylie, Todd N Wylie, Sung Hee Park, Ruiwen Zhou, Yin Cao, Stephanie A Fritz, Molly J Stout, Maria Cristina Vazquez Guillamet, Lei Liu

2020-Current year OA Pubs

Microbiome studies often seek to determine how the absolute abundances of individual taxa change across biological conditions, yet sequencing read counts are sample-specific scaled representations of those abundances. Because sampling depth can differ across samples, fold changes calculated directly from sequencing read counts do not generally represent absolute-abundance fold changes. Normalization methods attempt to account for these between-sample differences in sampling depth, but their accuracy depends on the reference used. In particular, total-sum scaling uses all taxa as the reference and can introduce compositional bias. Reference-based methods instead rely on taxa that are stable across conditions, but contamination of the …

Unlocking Cis-Regulatory Landscapes Across 500 Million Years Of Evolution And Disease Mechanisms, Tássia Mangetti Gonçalves, Casey L Stewart, Samantha D Baxley, Jason Xu, Kevin Boyer, Bijesh George, Daofeng Li, Chengran Yang, Harrison W Gabel, Xianhua Piao, Carlos Cruchaga, Yang E Li, Ting Wang, Oshri Avraham, Guoyan Zhao

2020-Current year OA Pubs

Genomic DNA encodes regulatory information that determines where, when, and to what extent genes are expressed. Theoretically, we should be able to identify these transcriptional "instructions" by examining genomic DNA sequence alone, yet this has remained challenging. Here we present the Vertebrate Regulatory MOdule Detector (VRMOD), a method that accurately predicts gene regulatory sequences using only the query genomic sequences. We applied VRMOD to 309 Ensembl genomes, generating a compendium of high-resolution, genome-position-fixed